<html>
<body style="padding:20px;width:650px;font-family:Times;">

<title>Cluster Methods</title>

<h2>Clustering Methods</h2>

This interface allows you to define a clustering method. This means
picking the basic algorithm, parameters, and a name. You can also
load a file defining your own clusters.

<h3>Prefix (required)</h3>

This is the prefix used for the clusters, e.g. if the 
cluster method is prefixed with "T1" and has three clusters, they will be named T1_1, T1_2, T1_3.
Since multiple groups of clusters can be added, this distinguishes them.

<h3>Name/Remark</h3>
These are shown on the Summary of viewMultiTCW, so should reflect the
method name and any parameters. For example, if orthoMCL was run with inflation 4,
then the Name could be "orthoMCL_4" and the Remark could be "inflation 4".

<h3>Method</h3>
From the drop-down menu, choose the algorithm to use. Current choices are:

<h5>OrthoMCL</h5>

OrthoMCL is an ortholog-detection package which has been included with TCW. Its
clustering is governed by the <b>Inflation</b> parameter; see www.orthomcl.org for more detail.
Larger inflation values lead to smaller clusters.

<h5>Transitive</h5>

The transitive method performs single-linkage clustering based on the pairwise links defined
by the blast output. In other words, two sequences will be in the same cluster if they have
at least one alignment in the blast file, and the clusters are formed by transitive closure
of these pairwise relations.
<p>
You can set two filter parameters <b>Similarity</b> and <b>Overlap cutoff</b>. 
The first is the same as blast "%Identity", and the second is the minimum overlap percentage, i.e.,
the overlap region must contain at least this percent of each sequence.

<h5>User Defined</h5>

Here you load a file defining your own groups. The format is as follows:
<pre>
1 DE|OlR_041805 DE|OlR_072235
2 ASM|demoASM_002 ASM|demoASM_003
...
</pre>
Each line has a group number followed by a space-separated list of the sequences in the group. 
Each group member starts with the project prefix followed by "|" (e.g. <tt>DE|</tt>), where
the prefix was selected during setup of the mTCW project.  
